From jw12 at sanger.ac.uk Tue Jan 19 05:41:12 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 19 Jan 2010 10:41:12 +0000 Subject: [DAS] DAS Workshop Registrations now Open (workshop date 7-9 April 2010) Message-ID: <9EDF4E46-15F8-434E-B557-2DE5906C4182@sanger.ac.uk> If you don't know about DAS and wish to know how to distribute your latest biological annotation to the world then the upcoming DAS workshop maybe for you. If you know about DAS and are maybe a DAS client developer then the upcoming DAS workshop is for you (as you will need to know about the upcoming DAS 1.6 Specification and how it may affect your software). For information on the workshop and registration please go to: http://www.ebi.ac.uk/training/handson/DAS_070410.html Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Mon Jan 25 12:08:18 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 25 Jan 2010 17:08:18 +0000 Subject: [DAS] deletion of servers/ new features in the registry Message-ID: <707B2571-7002-4D7A-A071-49396BFCB169@sanger.ac.uk> There are some new features in the DAS Registry one of them is a deletion/archiving of completely non-valid servers i.e. no green or yellow lights. Most servers that are scheduled for deletion have no response but some are still responding but without valid responses. An email should have been sent by the registry a long time ago if this is the case and you had alerts set to true. Servers set for deletion are shown with a red background if they have been completely invalid for 30 days or more and show the number of days left before being deleted (-numbers for those that have been invalid for more than 60 days). On Thursday this week all sources in this state will be removed unless you contact the registry by emailing dasregistry at sanger.ac.uk or me. Other new features are: added new 1.6 spec way of getting single source http://www.dasregistry.org/das/DS_blah * added ability for programmatic validation of das sources via www.dasregistry.org/validate/ e.g. http://www.dasregistry/validate/?url=http://das.sanger.ac.uk/das/otter_das/&testcode=22:19173435,19372173 minumum parameters needed are the url and the testcode * archive servers now implemented - so total number of servers will be reduced Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From biopython at maubp.freeserve.co.uk Fri Jan 29 05:36:40 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 29 Jan 2010 10:36:40 +0000 Subject: [DAS] [Bioperl-l] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: <320fb6e01001290236l1ad02515w403a19f94dbb6d15@mail.gmail.com> Hi all, This is a great topic but should be continue it on just the one mailing list? Is there a suitable BOSC list, or how about the general Open Bio list? On Thu, Jan 28, 2010 at 9:17 PM, Mark Wilkinson wrote: > > Brad, this sounds exciting! > > One thing strikes me, though - by asking for the sub-projects to propose > the "grand challenge" themselves the one thing you can guarantee is that > the "grand challenge" is solvable (or more likely, already solved!) > > Other "grand challenge" kinds of meetings have an independent third party > pose the problem that has to be solved, and then all groups work toward a > solution and compare their results. ?This would, IMO, be more revealing of > the "state of the art" in each Open-Bio project, and point out where the > weaknesses are that we should be focusing on... ?Someone (for example, > you!) could act as the moderator to ensure that the "grand challenge" was > at least a reasonable one, within the scope of what an Open-Bio project > *should* be able to solve... > > Just my CAD $0.02 > > Mark One possible problem with having Brad act as moderator is his ties to Biopython (plus it would be a shame if we'd be one man down for trying to solve the challenges - grin). Having a project representative "sign off" on the challenge might work - or simply the whole of the BOSC committee which is quite balanced. Alternatively some kind of panel of challenges does seem a good way to reduce individual project bias (as suggest by Scooter), but there will still need to be a judging committee. I'm curious what kind of challenges the BOSC committee had in mind - would something like taking a newly sequence bacteria and producing an automated annotation as a GenBank, EMBL, or GFF file be too ambitious for example? There are already several major projects to do this e.g. RAST http://rast.nmpdr.org/ Peter (@Biopython) From jw12 at sanger.ac.uk Fri Jan 29 07:12:58 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Fri, 29 Jan 2010 12:12:58 +0000 Subject: [DAS] Important : 1.6 Specification release Message-ID: Hello fellow DAS developers. We are now approaching the 2010 DAS workshop (April 7-9th http://www.ebi.ac.uk/training/onsite/DAS_070410.html) being held at the Sanger/EBI genome campus. The DAS 1.6 specification ( http://www.ebi.ac.uk/~aj/1.6_draft5/documents/spec.html ) has been written over the past year and we are approaching what we hope will be the final draft especially related to genomic DAS. It is our hope that client developers and data providers alike will develop and test the new 1.6 spec over the next couple of months. At the workshop we can discuss issues/improvements and decide on an official release date or just accept the new spec as official and release it. DAS clients will need to be able to handle the new 1.6 sources in some way - these sources should be identified by the correct header X-DAS- Version being sent (DAS/1.6 or DAS/1.6E) with any responses from a 1.6 server. The main change that will affect developers is the parent/parts usage instead of Group, but there are many other improvements and consolidations which the community had agreed last year would be useful. A list of changes taken from the spec is listed at the end of this email. Development so far: We have 1.6 specification development versions of Proserver (svn co https://proserver.svn.sourceforge.net/svnroot/proserver/branches/1.6-spec) and Dazzle (svn co http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle) available from SVN available for testing and development. The registry will now validate and accept 1.6 specification DAS sources, a list of which can be found using the web interface or requests to http://www.dasregistry.org/das1.6/sources note at the moment 1.6 sources will not be listed in the standard sources request (http://www.dasregistry.org/das/sources ) until the specification is official. Please register any new 1.6 sources you have created as examples to others. A new version of Dasobert will soon be available as part of the Biojava Version 3 development and a new version of Bio::Das::Lite. Some specimen 1.6 sources will be available in the registry soon as examples. CHANGES: This version mainly introduces concepts and extensions that are already in use but yet to be incorporated into the specification. Nonpositional annotations are now supported. Introduced the concept of "coordinate systems" and the DAS Registry. Relaxed the constraints on data source names. Clarified the use of HTTP and DAS status codes. Added requirement for clients to include specific request headers. All command responses are now described by RELAX NG schemas. New commands: sources, structure and alignment. These commands are taken from DAS 1.53E, with some changes. Deprecated commands: dsn, dna and link. Entry points command gained "paging", and other minor changes. Features command gained hierarchical referencing, in favour of groups. Several elements in the features command response are now optional. Features command gained "maxbins". Unified the format of segment XML across all commands. Added support for using ontologies in annotations. Stylesheets now support histograms, colour gradients and line plots, more colours, and are better characterised. The "toomany" glyph is deprecated. Clarified the content of attributes across several commands, such as segment versions. Thanks Jonathan Warren, Andy Jenkinson and the DAS developers at the Sanger/ EBI. Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Tue Jan 19 10:41:12 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 19 Jan 2010 10:41:12 +0000 Subject: [DAS] DAS Workshop Registrations now Open (workshop date 7-9 April 2010) Message-ID: <9EDF4E46-15F8-434E-B557-2DE5906C4182@sanger.ac.uk> If you don't know about DAS and wish to know how to distribute your latest biological annotation to the world then the upcoming DAS workshop maybe for you. If you know about DAS and are maybe a DAS client developer then the upcoming DAS workshop is for you (as you will need to know about the upcoming DAS 1.6 Specification and how it may affect your software). For information on the workshop and registration please go to: http://www.ebi.ac.uk/training/handson/DAS_070410.html Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Mon Jan 25 17:08:18 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 25 Jan 2010 17:08:18 +0000 Subject: [DAS] deletion of servers/ new features in the registry Message-ID: <707B2571-7002-4D7A-A071-49396BFCB169@sanger.ac.uk> There are some new features in the DAS Registry one of them is a deletion/archiving of completely non-valid servers i.e. no green or yellow lights. Most servers that are scheduled for deletion have no response but some are still responding but without valid responses. An email should have been sent by the registry a long time ago if this is the case and you had alerts set to true. Servers set for deletion are shown with a red background if they have been completely invalid for 30 days or more and show the number of days left before being deleted (-numbers for those that have been invalid for more than 60 days). On Thursday this week all sources in this state will be removed unless you contact the registry by emailing dasregistry at sanger.ac.uk or me. Other new features are: added new 1.6 spec way of getting single source http://www.dasregistry.org/das/DS_blah * added ability for programmatic validation of das sources via www.dasregistry.org/validate/ e.g. http://www.dasregistry/validate/?url=http://das.sanger.ac.uk/das/otter_das/&testcode=22:19173435,19372173 minumum parameters needed are the url and the testcode * archive servers now implemented - so total number of servers will be reduced Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From biopython at maubp.freeserve.co.uk Fri Jan 29 10:36:40 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 29 Jan 2010 10:36:40 +0000 Subject: [DAS] [Bioperl-l] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: <320fb6e01001290236l1ad02515w403a19f94dbb6d15@mail.gmail.com> Hi all, This is a great topic but should be continue it on just the one mailing list? Is there a suitable BOSC list, or how about the general Open Bio list? On Thu, Jan 28, 2010 at 9:17 PM, Mark Wilkinson wrote: > > Brad, this sounds exciting! > > One thing strikes me, though - by asking for the sub-projects to propose > the "grand challenge" themselves the one thing you can guarantee is that > the "grand challenge" is solvable (or more likely, already solved!) > > Other "grand challenge" kinds of meetings have an independent third party > pose the problem that has to be solved, and then all groups work toward a > solution and compare their results. ?This would, IMO, be more revealing of > the "state of the art" in each Open-Bio project, and point out where the > weaknesses are that we should be focusing on... ?Someone (for example, > you!) could act as the moderator to ensure that the "grand challenge" was > at least a reasonable one, within the scope of what an Open-Bio project > *should* be able to solve... > > Just my CAD $0.02 > > Mark One possible problem with having Brad act as moderator is his ties to Biopython (plus it would be a shame if we'd be one man down for trying to solve the challenges - grin). Having a project representative "sign off" on the challenge might work - or simply the whole of the BOSC committee which is quite balanced. Alternatively some kind of panel of challenges does seem a good way to reduce individual project bias (as suggest by Scooter), but there will still need to be a judging committee. I'm curious what kind of challenges the BOSC committee had in mind - would something like taking a newly sequence bacteria and producing an automated annotation as a GenBank, EMBL, or GFF file be too ambitious for example? There are already several major projects to do this e.g. RAST http://rast.nmpdr.org/ Peter (@Biopython) From jw12 at sanger.ac.uk Fri Jan 29 12:12:58 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Fri, 29 Jan 2010 12:12:58 +0000 Subject: [DAS] Important : 1.6 Specification release Message-ID: Hello fellow DAS developers. We are now approaching the 2010 DAS workshop (April 7-9th http://www.ebi.ac.uk/training/onsite/DAS_070410.html) being held at the Sanger/EBI genome campus. The DAS 1.6 specification ( http://www.ebi.ac.uk/~aj/1.6_draft5/documents/spec.html ) has been written over the past year and we are approaching what we hope will be the final draft especially related to genomic DAS. It is our hope that client developers and data providers alike will develop and test the new 1.6 spec over the next couple of months. At the workshop we can discuss issues/improvements and decide on an official release date or just accept the new spec as official and release it. DAS clients will need to be able to handle the new 1.6 sources in some way - these sources should be identified by the correct header X-DAS- Version being sent (DAS/1.6 or DAS/1.6E) with any responses from a 1.6 server. The main change that will affect developers is the parent/parts usage instead of Group, but there are many other improvements and consolidations which the community had agreed last year would be useful. A list of changes taken from the spec is listed at the end of this email. Development so far: We have 1.6 specification development versions of Proserver (svn co https://proserver.svn.sourceforge.net/svnroot/proserver/branches/1.6-spec) and Dazzle (svn co http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle) available from SVN available for testing and development. The registry will now validate and accept 1.6 specification DAS sources, a list of which can be found using the web interface or requests to http://www.dasregistry.org/das1.6/sources note at the moment 1.6 sources will not be listed in the standard sources request (http://www.dasregistry.org/das/sources ) until the specification is official. Please register any new 1.6 sources you have created as examples to others. A new version of Dasobert will soon be available as part of the Biojava Version 3 development and a new version of Bio::Das::Lite. Some specimen 1.6 sources will be available in the registry soon as examples. CHANGES: This version mainly introduces concepts and extensions that are already in use but yet to be incorporated into the specification. Nonpositional annotations are now supported. Introduced the concept of "coordinate systems" and the DAS Registry. Relaxed the constraints on data source names. Clarified the use of HTTP and DAS status codes. Added requirement for clients to include specific request headers. All command responses are now described by RELAX NG schemas. New commands: sources, structure and alignment. These commands are taken from DAS 1.53E, with some changes. Deprecated commands: dsn, dna and link. Entry points command gained "paging", and other minor changes. Features command gained hierarchical referencing, in favour of groups. Several elements in the features command response are now optional. Features command gained "maxbins". Unified the format of segment XML across all commands. Added support for using ontologies in annotations. Stylesheets now support histograms, colour gradients and line plots, more colours, and are better characterised. The "toomany" glyph is deprecated. Clarified the content of attributes across several commands, such as segment versions. Thanks Jonathan Warren, Andy Jenkinson and the DAS developers at the Sanger/ EBI. Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.